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The database in UGENE project view looks like as a tree with folders and files:

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  <img src="/wiki/download/attachments/8093781/Database in the Project.png"/>
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You can add a new folder to the database tree. To do it use the Add->Add folder database context menu item. To add a subfolder to the folder use the Add->Add folder folder context menu item. To delete a file or folder press the Delete button or drag'n'drop it to the Recycle bin. 

The objects in the database are read-only. To edit database data you need to export it to the project by the Export/Import object context menu. If the database data will be updated outside your database data will be updated automatically.